Dear Mark, I looked at gromacs mail list but I could not find a proper solution .Whatshould I add to the .top file? Please look at the following reconstructed1 .top and reconstructed1 .top files
I have error as the following reconstructed1 .top file: *Fatal error:* moleculetype CU1 is redefined I have error as the following reconstructed2 .top file: *Fatal error:* No such moleculetype CL- * Original .top file:* ; Include topology for ions #include "gromos43a1.ff/ions.itp" [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 41779 *reconstructed1 .top file* ; Include topology for ions #include "gromos43a1.ff/ions.itp" *#include "ions.itp"* [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 4177*1* CL- *8* *reconstructed2 .top file* ; Include topology for ions #include "gromos43a1.ff/ions.itp" ** [ system ] ; Name GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water [ molecules ] ; Compound #mols Protein_chain_P 1 Protein_chain_L 1 Protein_chain_H 1 SOL 10 SOL 127 SOL 157 SOL 4177*1* CL- *8* 25 Ocak 2011 10:49 tarihinde Mark Abraham <mark.abra...@anu.edu.au> yazdı: > > > On 01/25/11, *ahmet yıldırım * <ahmedo...@gmail.com> wrote: > > Hi, > > In my simulation, total charge of the system is a noninteger number (System > has non-zero total charge: 8.000004e+00). I neutralized it with 8 chlorine > atoms. > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr > > Fatal error: > moleculetype CU1 is redefined > is it some thing wrong? > > > ions.itp defines molecule types for ions. Molecule types cannot be > redefined. When you #included ions.itp GROMACS thought you were doing > illegal redefinitions. Look back in the .top to find the original > definitions, and then take suitable action. > > Mark > > > > > Below is the first and final version of the .top file: > > First topol.top File > *....* > [ molecules ] > ; Compound #mols > Protein_chain_P 1 > Protein_chain_L 1 > Protein_chain_H 1 > SOL 10 > SOL 127 > SOL 157 > SOL 41779 > ** > > Final topol.top File > *#include "ions.itp"* > > [ molecules ] > ; Compound #mols > Protein_chain_P 1 > Protein_chain_L 1 > Protein_chain_H 1 > SOL 10 > SOL 127 > SOL 157 > SOL *41771* > *CL- 8* > > > > > > > -- > Ahmet YILDIRIM > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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